tbuckley/cabot-search huggingface dataset:
Abstract 1947: Clinical and genomic correlates with genetic ancestry in lung squamous cell carcinoma
Authors: Sejal Jain, Alexandria G. Yao, Diane Allen-Gipson, Fatemeh Momen-Heravi, Alison M. Taylor
Journal: Cancer Research (2023)

Abstract Many translational studies suggest racial and ethnic survival disparities in lung squamous cell carcinoma (LSCC), with self-identified African-Americans showing significantly lower overall survival and progression-free survival than self-identified Caucasians. However, potential clinical and genomic factors contributing to this disparity have yet to be elucidated. Using clinically annotated genomic data from 501 LSCC tumor samples in the Cancer Genome Atlas (TCGA), we compared clinical data, gene expression profiles, mutations, and focal and arm-level copy number changes from tumors across ancestral groups to identify significantly differential events. Within this dataset, patients of AFR ancestry had worse survival and progression-free survival then patients of EUR ancestry. We applied the Cox Proportional Hazards model to predict overall and progression-free survival as functions of genetic ancestry alongside other genetic, molecular, and clinical variables. We found a significant difference in metastatic stage between tumors from patients of African (AFR) and European (EUR) ancestry, which was significant in predicting survival. Compared to tumors from EUR patients, tumors from AFR patients featured increased chromosome arm 8q gain and more frequent amplification of genetic locus chr8q24, which contains proto-oncogene MYC. Expression of MYC target genes was also significantly increased in AFR samples relative to EUR samples. These findings may suggest a role for the MYC pathway in differential cancer progression. We found more frequent amplification of genetic loci chr22q11 and chr16p11 in AFR samples compared to EUR samples. We identified top differentially mutated genes between groups, of which SPRR3, PDGFA, FRS3, and C21orf62 correlate with survival. We also found immune signaling gene sets enriched in the EUR group by gene set expression analysis (GSEA). These results suggest potential genetic and clinical factors implicated in racial survival disparities. Further studies and more diverse sampling of cancer patient populations are required to validate these differences and elucidate patient-specific treatment modalities. Citation Format: Sejal Jain, Alexandria G. Yao, Diane Allen-Gipson, Fatemeh Momen-Heravi, Alison M. Taylor. Clinical and genomic correlates with genetic ancestry in lung squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1947.
Abstract 1517: Genetic characterization of normal pancreas tissue using single-cell technology
Authors: Elias-Ramzey R. Karnoub, Haochen Zhang, Shigeaki Umeda, Ignas Masilionis, Ronan Chaligné, Christine Iacobuzio-Donahue
Journal: Cancer Research (2023)

Abstract Mechanisms behind the evolution of normal pancreas tissue into pancreatic ductal adenocarcinoma (PDAC) are still poorly understood. More thorough characterization of mutational processes and development of clones is possible with single-cell DNA sequencing (scDNA-seq) of normal pancreas tissue. We developed a custom panel with 596 amplicons targeting over 200 genes known to be important in PDAC for use with Mission Bio’s Tapestri platform. We have recently optimized this method with nuclei which have been extracted from thirty frozen normal pancreas tissues, each from a different patient. Of these tissues, twenty-five were derived from rapid autopsies of patients with brain tumors to minimize the possibility of tumor cells being present in the pancreas. Normal pancreas tissue was verified by hematoxylin and eosin staining. Nuclei were extracted using the S2 Genomics Singulator 100 and counted with DAPI using the Countess 3 FL to ensure the concentration was adequate and that the sample was clean without excessive debris before library preparation and sequencing. Bulk whole exome sequencing (WES) and digital droplet polymerase chain reaction (ddPCR) were performed on several of these sample to validate certain mutations seen in scDNA-seq. Patients of a variety of ages ranging from five to 74 and with various risk factors including smoking and diabetes were chosen to better understand the impact on clonal expansion and genetic patterns present in normal pancreas tissue. For each of the thirty samples, an average of 2464 good quality nuclei were sequenced with over 70 reads per cell per amplicon on average. Mutations that were present in high quantities of cells were confirmed with WES and ddPCR. We found that older patients and patients that either smoke or those with diabetes had not only an increased number of mutations, but each individual cell, on average, had a significantly higher mutation count. The associated clones were also much greater in size in the higher-risk patients’ tissues. Furthermore, there was an increase in heterogeneity in the form of mutually exclusive clusters of cells. These results highlight the effects of various risk factors on normal pancreas tissue and potentially describe novel mechanisms of tumorigenesis. Citation Format: Elias-Ramzey R. Karnoub, Haochen Zhang, Shigeaki Umeda, Ignas Masilionis, Ronan Chaligné, Christine Iacobuzio-Donahue. Genetic characterization of normal pancreas tissue using single-cell technology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1517.
Abstract 3382: Detection of CTCs using a micro-channel combined fluid dynamics and electrophoresis in colorectal cancer
Authors: Ryo Ohta, Takeshi Yamada, Nobuhiko Taniai, Hiroshi Yoshida
Journal: Cancer Research (2023)

Abstract Background: Circulating tumor cells (CTCs) are tumor cells that can be isolated from peripheral blood. Investigation of CTCs might allow comprehensive studies at the DNA, RNA, and protein. However, fewer CTCs generally can be collected from patients with colorectal cancer, limiting the possibility of clinical applications of CTC analysis despite the development of many different methods. We have developed a micro-channel device that integrates hydrodynamic filtration (HDF) capable of size separation and dielectrophoresis (DEP) capable of electrical property separation, using peripheral blood from colorectal cancer patients. Method: A separation test was performed using a whole peripheral blood sample obtained from colorectal cancer patients with KRASmutation in the tumor tissue. The sample blood was diluted 2-fold with PBS, and red blood cells and plasma were removed using HDF. After that, Leukocytes and CTCs were separated in the same channel by DEP. DNA was extracted from CTCs (port 1) and leucocyte fraction (port 2), and KRAS mutations were detected using droplet digital PCR. In order to evaluate the separated fractions, microwell slide was used for evaluation by nuclear staining, CD45 and EpCAM antibody staining. Results: 52 colorectal cancer patients were participated. The median age of patients was 71 years, 38 (73%) were male. Twenty-eight (53.9%) had colon cancers. Four stage III and 48 stage IV patients were included. The quality of DNA extracted from all patients were suitable for molecular genetic analysis. The DNA concentration of port 1 was significantly lower than that of port 2 (371 ng/mL vs 36667 ng/mL, P&amp;lt;0.001). Using droplet digital PCR, KRAS mutations were detected in the port 1 of 8 (15.4%) patients and in port 2 of 15 (28.8%) patients. In 35.5% of patients, KRAS mutations were detected in either port 1 or port 2. Conclusion: This device does not require pretreatment and is easy to extract CTCs. Since CTCs are contaminated with the leukocyte fraction, it is necessary to improve the accuracy of CTCs collection by adjusting the conditions of DEP. Citation Format: Ryo Ohta, Takeshi Yamada, Nobuhiko Taniai, Hiroshi Yoshida. Detection of CTCs using a micro-channel combined fluid dynamics and electrophoresis in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3382.
Abstract 261: Whole genome sequencing provides a more comprehensive genetic characterization of lung cancer compared to a targeted panel sequencing
Authors: Ji-Hyung Park, Young Tae Kim, Erin Connolly-Strong, Young Seok Ju
Journal: Cancer Research (2023)

Abstract Non-small cell lung cancer (NSCLC) remains the leading cause of cancer death in the United States despite a decline in mortality. Adenocarcinoma of the lung usually evolves from the mucosal glands and represents about 40% of all lung cancers. A significant proportion of lung adenocarcinoma patients present alterations in oncogenic driver genes. Next-Generation Sequencing (NGS) allows the sequencing of several genomic regions in a single test. There are multiple NGS approaches including Targeted Panel Sequencing (TPS), Whole Exome Sequencing (WES), and Whole Genome Sequencing (WGS). Methods: The detection of actionable genomic mutations in 60 lung adenocarcinoma surgical specimens was evaluated through two NGS approaches TPS and WGS. TPS was performed using the Seoul National University Hospital (SNUH) TPS consisting of 75 total genes, with a total coverage of 1.92Mb (exon 0.69Mb, intron 1.23Mb). WGS was performed using Illumina’s NovaSeq 6000 platform and data were processed with BWA and variant callers including Mutect2 and Delly. Functional mutations were determined by Ensembl VEP, while putative driver mutations were identified via the Genome Insight pipeline (San Diego). Results: A total of 120 driver mutations were detected by TPS. WGS identified 114 out of the 120 driver mutations (95% match). An additional 9 driver mutations were detected by WGS, along with thousands of additional non-driver mutations. (Table 1) Conclusion: An NGS-based approach allows for the identification of actionable molecular changes which leads to more informed clinical decision making. These results validate that Genome Insight’s WGS workflow and pipeline are comparable to TPS in detecting key driver mutations. Furthermore, this study demonstrated that WGS provides a more comprehensive genetic characterization of lung cancer, which may impact the therapeutic options and patients’ prognosis. Table 1. Driver mutations # of mutations detected by TPS # of mutations detected by WGS Detected by TPS EGFR 20 19 KRAS 9 9 TP53 30 30 Fusion oncogenes 17 17 PIK3 genes 1 1 BRAF 2 2 Secondary drivers detected by TPS 41 36 Sub-total 120 114 Missed by TPS Other drivers not detected by TPS 0 9 Total 120 123 Citation Format: Ji-Hyung Park, Young Tae Kim, Erin Connolly-Strong, Young Seok Ju. Whole genome sequencing provides a more comprehensive genetic characterization of lung cancer compared to a targeted panel sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 261.
Abstract SY12-04: Lowering the TCR signaling threshold with a DGKa/z dual inhibitor potentiates anti-tumor immunity
Authors: Stephanie K. Dougan
Journal: Cancer Research (2023)

Abstract Checkpoint blockade immunotherapies expand neoantigen- or virus-specific T cells, and poor responsiveness to immunotherapy is associated with lower mutational burden in tumors of non-viral origin. Although mouse models demonstrate that lower affinity T cells recognizing self-antigens can contribute to tumor control if sufficiently activated, therapeutic options for enhancing T cell priming are limited. Diacylglycerol kinases (DGKs) suppress DAG signaling by converting DAG to phosphatidic acid, thereby attenuating pathways downstream of TCR signaling. Using a novel dual DGKa/z inhibitor (DGKi), tumor-specific CD8 T cells with different affinities (TRP1high and TRP1low), and a series of altered peptide ligands, we demonstrate that inhibition of DGKa/z can lower the signaling threshold for T cell priming. TRP1high and TRP1low CD8 T cells produced more IL-2 and IFNγ in the presence of cognate antigen and DGKi. Effector TRP1high- and TRP1low-mediated cytolysis of tumor cells with low antigen load was MHC-restricted, mediated by IFNg and augmented by DGKi. Adoptive T cell transfer into mice bearing pancreatic or melanoma tumors synergized with single-agent DGKi or DGKi and αPD1, with increased expansion of low affinity T cells and increased cytokine production observed in tumor infiltrates of treated mice. Collectively, our findings highlight DGKa/z as therapeutic targets for augmenting tumor-specific CD8 T cell function. Citation Format: Stephanie K. Dougan. Lowering the TCR signaling threshold with a DGKa/z dual inhibitor potentiates anti-tumor immunity. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr SY12-04.
Abstract 1594: SMARCA2 (BRM) degraders promotes differentiation and inhibit proliferation in AML models
Authors: Anjana Agarwal, Olusola Peace Osinubi, Komali Vykuntam, Norman Fultang, Neha Bhagwat, Diane Heiser, Kris Vaddi, Koichi Ito, Peggy Scherle
Journal: Cancer Research (2023)

Abstract Dysregulated cellular differentiation is a major pathological feature of myeloid malignancies such as acute myeloid leukemia (AML). Targeting cellular differentiation programs has emerged as a novel therapeutic approach to treat patients with AML. Advantages of such differentiation therapy may include fewer systemic side-effects as well as opportunities to target leukemic stem cells (LSCs) and a broader range of clonal populations, likely resulting in lower frequencies of resistance and relapse in AML patients. The success of ATRA and decitabine in subsets of AML patients has proven that inducing differentiation can play a critical role in long-term durable responses. More agents targeting epigenetic regulators have been increasingly studied as differentiation inducers, including LSD1, DNMT1, Menin, and BET inhibitors. Recently, targeting SWI/SNF chromatin remodeling complexes has also been shown to regulate key leukemic gene expression signatures and induce AML differentiation. Small molecule inhibitors as well as gene knockdown for ATP-dependent SWI/SNF subunits SMARCA2 (BRM) and SMARCA4 (BRG1) are associated with re-direction of oncogenic transcriptional regulation to drive cellular differentiation and apoptosis in AML models. We have previously described the activity of highly potent, bispecific SMARCA2 degraders that efficiently promote SMARCA2 protein degradation in preclinical models. In the present study, we investigated the effects of our SMARCA2 selective degraders in AML models. Treatment with SMARCA2 degraders significantly inhibits AML cell line proliferation in vitro with IC50 ranging from 10 to 50 nM. In the SMARCA2 degrader treated cells, expression of PU.1 (SPI1), a key transcription factor in myeloid leukemias, was downregulated. In an in vivo OCI-AML3 xenograft model, treatment with a SMARCA2 selective degrader showed moderate tumor growth inhibition accompanied by robust increases in monocytic maturation markers CD11b and CD14. Further analyses of SMARCA2 degrader effects on global transcriptome and AML immunophenotypes as well as combination effects with other therapies are currently in progress. These findings highlight the potential of SMARCA2 degraders to target AML differentiation blocks and to improve the effectiveness of other therapeutic agents such as decitabine and venetoclax in AML patients. Citation Format: Anjana Agarwal, Olusola Peace Osinubi, Komali Vykuntam, Norman Fultang, Neha Bhagwat, Diane Heiser, Kris Vaddi, Koichi Ito, Peggy Scherle. SMARCA2 (BRM) degraders promotes differentiation and inhibit proliferation in AML models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1594.
Abstract 5950: Ccr2+ monocyte derived macrophages influence trajectories of acquired therapy resistance in BRAF-mutant melanoma
Authors: Dahihm Kim, Luye An, Jiwon Moon, Andrew White
Journal: Cancer Research (2023)

Abstract Therapies targeting oncogene addiction have had a tremendous impact on patient care, but drug resistance continues to be problematic. One method to deal with this challenge entails extending the scope of anti-cancer treatment beyond tumor cells by additionally altering their tumor microenvironment. Understanding how the tumor microenvironment can contribute to the evolution of diverse resistance pathways could aid in the rational design of sequential treatments that enforce pressure towards a more predictable resistance trajectory. Tumor associated macrophages often support neoplastic growth and are frequently the most abundant immune cell found in tumors. Here, we used clinically relevant in vivo Braf-mutant melanoma models and Ccr2-RFP; Cx3cr1-GFP mice to track the long-term changes in tumor cells and macrophages under targeted therapy with Braf/Mek inhibitors. We assessed the dynamic evolution of the macrophage population generated by therapy pressure-induced stress. During the onset of a drug-tolerant persister state, Ccr2+ macrophage infiltration rises, underscoring a prominent role at this point in melanoma evolution for development of drug-resistance. Importantly, we show that a lack of melanoma infiltrating Ccr2+ macrophages delays onset of resistance. In this case, rebounded tumor cells from Ccr2 knockout recipients favor the evolution of cell-extrinsic mediated resistance mechanisms, which can be reversed when these adapted melanoma cells are relocated to a microenvironment with functional Ccr2. Conversely, Ccr2 presence promotes development of cell-intrinsic drug resistance with a stable phenotype in rebounded tumor cells. Overall, this demonstrates that the development of resistance may be manipulated and directed to improve timing and probability of relapse. Citation Format: Dahihm Kim, Luye An, Jiwon Moon, Andrew White. Ccr2+ monocyte derived macrophages influence trajectories of acquired therapy resistance in BRAF-mutant melanoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5950.
Abstract 5988: A non-canonical CDK9 complex mediates endocycling in polyaneuploid cancer cell (PACC) state
Authors: Cheng-fan Lee, Michael Loycano, Luke LOFTUS, Laurie Kostecka, Melvin Li, Sarah Amend, Kenneth Pienta
Journal: Cancer Research (2023)

Abstract Once prostate cancer has spread from its primary site, treatment is limited to systemically administered therapy. While tumors initially respond to these therapies, eventually, all therapies fail, and the tumor recurs. Ours and others' recent studies have shown the presence of a universal mechanism of resistance: accession of the polyaneuploid cancer cell (PACC) state. The PolyAneuploid Transition (PAT) is initiated when a cancer cell is subjected to external stress, including therapy (we have tested three classes of chemotherapy and radiation), and accesses an alternative non-mitotic cell cycle known as endocycling, resulting in a greater-than-G2 polyploidization of the aneuploid genome (polyaneuploidy). While in this pro-survival PACC state, we have shown that cells are resistant to all forms of cytotoxic therapy. Initial RNA sequencing of cells that have accessed the PACC state in response to multiple classes of chemotherapy, including docetaxel and cisplatin, demonstrate a remodeled transcriptional profile that is distinct from control cultures. We hypothesize that accession of the resistance-mediating PACC state requires transcriptional remodeling. Our data show that cells in the PACC state had increased overall transcriptional activity. The multi protein complex pTEFB (positive transcription elongation factor) is a critical driver of RNA Polymerase II function and is composed of multiple subunits, including CDK9, a cyclin regulatory subunit, and a transcription factor. CDK9 phosphorylation was significantly elevated during accession and persistence in the PACC state. Genetic inhibitionof CDK9 by siRNA led to decreased expression of cyclin A which plays a role in S phase, both in the mitoticcycle and in the PACC endocycle. Interestingly, despite increased CDK9 levels, known CDK9 pTEFb complex members cyclin T1 and BRD4 were both decreased in cells in the PACC state. We treated cancer cells induced to enter the PACC state upon exposure to cisplatin with pharmaceutical inhibitors of CDK9, Flavopiridol and Fadraciclib. Combination of CDK9 inhibition with chemotherapy showed a suppressive effect on the PACC population. Our findings therefore suggest that a non-canonical CDK9 complex could be critical role for the endocycling to access and maintain the PACC state and represents a therapeutic candidate to eliminate the resistance-mediating PACC state. Citation Format: Cheng-fan Lee, Michael Loycano, Luke LOFTUS, Laurie Kostecka, Melvin Li, Sarah Amend, Kenneth Pienta. A non-canonical CDK9 complex mediates endocycling in polyaneuploid cancer cell (PACC) state. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5988.